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The SENSEI generic in situ interface is an API that promotes code portability and reusability. From the simulation view, a developer can instrument their code with the SENSEI API and then make make use of any number of in situ infrastructures. From the method view, a developer can write an in situ method using the SENSEI API, then expect it to run in any number of in situ infrastructures, or be invoked directly from a simulation code, with little or no modification. This paper presents the design principles underlying the SENSEI generic interface, along with some simplified coding examples.

With the rapidly increasing reliance of life sciences research on digital data and sophisticated computational analysis techniques, the ability to reproduce findings generated by in-silico data analysis workflows is of increasing importance to the scientific community. However, challenges to reproducibility arise from the heterogeneity of approaches available to workflow definition and enactment. In this work, we explore the requirements of ‘digital reproducibility’ of genomic data analysis by implementing a complex but extensively used bioinformatics workflow using three widely adopted approaches that differ markedly in their implementation. We use these case studies to identify implicit and explicit assumptions present in each of the workflow implementations and then propose a comprehensive breakdown of reproducibility requirements that can inform a more structured, assumption-free approach to implementing highly reproducible genomic analyses.

Background Free vascularized bone flaps are widely recognized as the optimal reconstruction for patients who undergo mandibular resection. The fibula-free flap is currently considered the gold standard, workhorse flap for mandibular reconstruction. Although previous studies have analysed individual success of each flap type, few have compared iliac- and fibula-free flaps. Methods A systematic review of the literature was conducted in line with the PRISMA protocol searching the PubMed and EBSCO databases. Twenty-four studies were included as per predetermined inclusion criteria. Double-arm random effect meta-analysis was conducted with STATA 12, and single-arm meta-analysis was conducted utilizing Meta-XL. Results The results of this meta-analysis confirm that there is no significant difference in total flap loss between fibula- and iliac-free flap reconstruction of mandibular defects. In terms of recipient site complication, there was a significantly higher risk of delayed healing and suture line breakdown in the iliac flap group (P = 0.05). Donor site complications showed a trend towards being higher in the fibula flap group. Osseointegrated dental implant loss in fibula flaps was higher than in iliac flaps (5.3% compared with 1.7%). Conclusion Both iliac- and fibula-free flaps should be considered for use in mandibular reconstruction. We suggest the iliac crest as the first choice for mandibular angle or body defects (better contour match) or also defects requiring greater soft-tissue bulk for intra-oral lining. The fibula flap is best when bony length is required such as in subtotal or total mandibulectomy.

Background Deep sternal wound infection (DSWI) is a rare but life-threatening complication following cardiac surgery associated with increased morbidity and mortality. Management of these patients has evolved over the years and can include sternal rewiring, mediastinal irrigation, negative-pressure wound therapy (NPWT) dressing or repair with flaps. We reviewed changes in our management of DSWI and outcomes. Methods Using the Australian and New Zealand Society of Cardiac and Thoracic Surgeons database, 5472 underwent cardiac surgery at St Vincent's Hospital, Melbourne, and 42 were identified as developing DSWI requiring re-operation between June 2002 and September 2014. Data were collected pertaining to risk factors for DSWI, management strategies and outcomes. Patients were compared from a period prior to NPWT dressing use (June 2002–February 2006, n = 14) and since the NPWT has been used regularly in the management of DSWI (from March 2006, n = 28). Patients were also compared based on the requirement for flap closure of their sternal wound. Results Because of the widespread use of NPWT dressings, there is a trend towards fewer sternal infections requiring flap closure (25 versus 42.8%) and less post-operative complications after definitive closure (7.1 versus 28.6%). Before and after widespread NPWT use, patients require similar number of re-operations before closure and have no significant differences in time to definitive closure or length of hospital stay. Conclusion The use of NPWT dressings as a bridge to definitive closure may reduce the need for more burdensome flap reconstruction, does not delay definitive reconstruction or prolong hospital stay and may reduce post-reconstruction complications requiring re-operation.

Objective The objective of this article is to provide a review of Transformative Learning Theory and identify its application to pharmacy education. Background The pharmacy profession continues to struggle with the transition from product-centered to patient-centered service delivery. Revised Accreditation Council for Pharmacy Education (ACPE) learning outcome requirements, as well as new technology, government regulations, and reimbursement models, may soon mean obsolescence for pharmacists who do not possess the necessary introspective and metacognitive abilities that can lead to mature patient-centered skill sets. Method Snowball method was used to review Transformative Learning Theory and find strategies to apply to teaching in Pharmacy. Conclusion Pharmacy educators can use Transformative Learning Theory or aspects of the theory to develop specific self-awareness and metacognitive skills needed by all health care professionals. In addition, transformative teaching can provide a powerful context not only for professional education but also for lifelong learning. Transformative teaching is a pedagogy that makes use of Transformative Learning concepts.

Modern organizations need to develop 'digital forensic readiness' to comply with their legal, contractual, regulatory, security and operational obligations. A review of academic and practitioner literature revealed a lack of comprehensive and coherent guidance on how forensic readiness can be achieved. This is compounded by the lack of maturity in the discourse of digital forensics rooted in the informal definitions of key terms and concepts. In this paper we validate and refine a digital forensic readiness framework through a series of expert focus groups. Drawing on the deliberations of experts in the focus groups, we discuss the critical issues facing practitioners in achieving digital forensic readiness.

This article considers the processes of musical learning that take place across formal, non-formal and informal contexts and spaces. Building on notions of embodied knowledge, identity and culture within education studies, specifically the concept of ‘musical habitus’, this article explores processes of access, inclusion and appropriation of music learning environments. Based on focus group discussions with a diverse group of young Londoners (aged 16–25 years) taking part in Wired4Music, a publicly funded youth leadership programme, the article considers definitions and the significance of music and learning places to these emerging musicians. This includes the processes through which musical learning takes place and the relevant factors that contribute to productive learning. Often operating within a context of subsidised arts provision, these perspectives are also considered within the current cultural policy landscape in England. Participants described implicit and explicit processes of exclusion to some formal music education settings and approaches, whereby a less formal though still intentional approach to learning was enacted in response. This included re-appropriating spaces and creating music in communities of practice, embracing multi-modal approaches to learning across art forms and genres and self-directing learning opportunities. These findings strongly resonate with studies which have critically appraised the specific sites and spaces where education takes place, as well as those suggesting that theories of identity, taste and cultural consumption should also be considered in education praxis, whether formal, non-formal or informal.

Purpose. Negative-pressure wound therapy (NPWT) is increasingly used for primary surgical incisions despite the paucity of evidence. Study objectives were to assess the use of NPWT on surgical sites to prevent infections and other wound complications after elective primary hip arthroplasty and to consider feasibility of a larger trial. Methods. A nonmasked, randomized controlled pilot trial. Patients were recruited preoperatively from the preadmission clinic of an Australian hospital during 2013-2014. Computer-generated randomization was performed with allocation concealed until completion of surgery. The intervention group received NPWT (PICO) while the control group received the standard care hydrocolloid, reinforced with 2 absorbent dressings. Patients were followed for 6 weeks for postoperative complications (infection, length of stay, readmission) and skin complications (bruising, seroma, hematoma, dehiscence). Feasibility end points included numbers recruited, randomized, and followed up; fidelity; and costs. Results. Of 77 people approached, 76 were recruited, and 70 were randomized. Of 35 in the negative-pressure group, 2 received the standard dressing. Attrition at 6 weeks exceeded 10% in both groups. Dressing costs were lower in the control group ($3.01/d vs $38.40/d); SSI incidence was 2/35 in the NPWT and 3/35 in the control group (intention to treat: risk ratio [RR] = 0.67; 95% confidence interval [CI] = 0.12-3.7; P = .65). NPWT patients experienced more postoperative wound complications (RR = 1.6; 95% CI = 1.0-2.5; P = .04). Conclusion. A reduction of 3% in SSI incidence suggests that a definitive trial requires approximately 900 patients per group. Yet there is uncertainty around the benefit of NPWT after elective hip arthroplasty.

O presente artigo tem por objetivo divulgar os resultados obtidos com o mapeamento geomorfologico na bacia do ribeirao Santa Barbara (MG) e elaboracao da carta geomorfologica correspondente, editada na escala de 1/50.000, em consonância ao plano metodologico estabelecido pelo Instituto Brasileiro de Geografia e Estatistica. O trabalho deu conta de mapear unidades geomorfologicas ordenadas em padroes de formas semelhantes segundo os modelados de dissecacao e agradacao identificados e seus aspectos morfometricos fundamentais (declividade, profundidade de dissecacao e dimensao interfluvial). Em um segundo nivel de abordagem, foi empreendida a insercao de simbolos representativos de feicoes morfologicas e processos atuais (escarpas de falha, ravinas, focos de arenizacao, capturas), permitindo uma interpretacao abrangente do relevo da area de estudo em suas formas e processos, preteritos e atuais.

Aberrant DNA methylation is a key feature of breast carcinoma. We aimed to test the association between breast cancer risk and epigenome-wide methylation in DNA from peripheral blood. Nested case-control study within the prospective Melbourne Collaborative Cohort Study. DNA was extracted from before-diagnosis blood samples (420 incident cases and matched controls). Methylation was measured with the Illumina Infinium Human Methylation 450 BeadChip array. Odds ratio (OR) for epigenome-wide methylation, quantified as the mean beta values across the CpGs, in relation to breast cancer risk were estimated using conditional logistic regression. Overall, the OR for breast cancer was 0.42 (95% CI 0.20-0.90) for the top versus bottom quartile of epigenome-wide DNA methylation and the OR for a one standard deviation increment was 0.69 (95% CI 0.50-0.95; test for linear trend, p = 0.02). Epigenome-wide DNA methylation of CpGs within functional promoters was associated with an increased risk, whereas epigenome-wide DNA methylation of genomic regions outside promoters was associated with decreased risk (test for heterogeneity, p = 0.0002). The increased risk associated with epigenome-wide DNA methylation in functional promoters did not vary by time between blood collection and diagnosis, whereas the inverse association with epigenome-wide DNA methylation outside functional promoters was strongest when the interval from blood collection to diagnosis was less than 5 years and weakest for the longest interval. Epigenome-wide methylation in DNA extracted from peripheral blood collected before diagnosis may have potential utility as markers of breast cancer risk and for early detection.

BI-RADS for mammography and ultrasound subdivides category 4 assessments by likelihood of malignancy into categories 4A (2% to ≤ 10%), 4B (10% to ≤ 50%), and 4C (50% to95%). Category 4 is not subdivided for breast MRI because of a paucity of data. The purpose of the present study is to determine the utility of categories 4A, 4B, and 4C for MRI by calculating their positive predictive values (PPVs) and comparing them with BI-RADS-specified rates of malignancy for mammography and ultrasound.All screening breast MRI examinations performed from July 1, 2010, through June 30, 2013, were included in this study. We identified in medical records prospectively assigned MRI BI-RADS categories, including category 4 subdivisions, which are used routinely in our practice. Benign versus malignant outcomes were determined by pathologic analysis, findings from 12 months or more clinical or imaging follow-up, or a combination of these methods. Distribution of BI-RADS categories and positive predictive value level 2 (PPV2; based on recommendation for tissue diagnosis) for categories 4 (including its subdivisions) and 5 were calculated.Of 860 screening breast MRI examinations performed for 566 women (mean age, 47 years), 82 with a BI-RADS category 4 assessment were identified. A total of 18 malignancies were found among 84 category 4 and 5 assessments, for an overall PPV2 of 21.4% (18/84). For category 4 subdivisions, PPV2s were as follows: for category 4A, 2.5% (1/40); for category 4B, 27.6% (8/29); for category 4C, 83.3% (5/6); and for category 4 (not otherwise specified), 28.6% (2/7).Category 4 subdivisions for MRI yielded malignancy rates within BI-RADS-specified ranges, supporting their use for benefits to patient care and more meaningful practice audits.

This article documents a productive partnership between a local archives and a community college that resulted in an enhanced learning experience for students and provided an opportunity to connect the archives with an underserved audience. Students were asked to creatively commemorate the life of a soldier or nurse who served in the First World War using archival military service files as inspiration. Through the project, students developed their research and communication skills and became familiar with the functions of an archives and the utility of working with primary source documents. The project successfully blended archival research with a creative pedagogical approach and serves as a model that could be adapted to fit a diverse range of subjects, using a variety of archival collections.

Background Computational bioinformatics workflows are extensively used to analyse genomics data, with different approaches available to support implementation and execution of these workflows. Reproducibility is one of the core principles for any scientific workflow and remains a challenge, which is not fully addressed. This is due to incomplete understanding of reproducibility requirements and assumptions of workflow definition approaches. Provenance information should be tracked and used to capture all these requirements supporting reusability of existing workflows. Results We have implemented a complex but widely deployed bioinformatics workflow using three representative approaches to workflow definition and execution. Through implementation, we identified assumptions implicit in these approaches that ultimately produce insufficient documentation of workflow requirements resulting in failed execution of the workflow. This study proposes a set of recommendations that aims to mitigate these assumptions and guides the scientific community to accomplish reproducible science, hence addressing reproducibility crisis. Conclusions Reproducing, adapting or even repeating a bioinformatics workflow in any environment requires substantial technical knowledge of the workflow execution environment, resolving analysis assumptions and rigorous compliance with reproducibility requirements. Towards these goals, we propose conclusive recommendations that along with an explicit declaration of workflow specification would result in enhanced reproducibility of computational genomic analyses. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1747-0) contains supplementary material, which is available to authorized users.

The term Provenance is referred to as ‘The beginning of something’s existence; something’s origin’ Or ‘A record of ownership of a work of art or an antique, used as a guide to authenticity or quality’. Provenance tracking is crucial in scientific studies where workflows have emerged as an exemplar approach to mechanize data-intensive analyses. Gil et al. analyze challenges of scientific workflows and concluded that formally specified workflow helps‘accelerate the rate of scientific process’ and facilitates others to reproduce the given experiment provided that provenance of end-to-end process at every level is captured.We have implemented exemplar GATK variant calling workflow using three approaches to workflow definition namely Galaxy, CWL and Cpipe to identify assumptions implicit in these approaches. These assumptions lead to limited or no understanding of reproducibility requirements due to lack of documentation and comprehensive provenance tracking and resulted in identification of provenance information crucial for genomic workflows.CWL provides a declarative approach to workflow declaration making minimal assumptions about precise software environment, base software dependencies, configuration settings, alteration of parameters and software versions. It aims to provide an open source extensible standard to build flexible and customized workflows including intricate details of every process. It facilitates capture of information by supporting declaration of requirements, `cwl:tool` and checksums etc. Currently, there is no mechanism to gather the produced information as a result of a workflow run into one bundle for future use. We propose to demonstrate the implementation of a module for CWL.

Modern scientific, engineering and medical computational simulations, as well as experimental and observational data sensing/measuring devices, produce enormous amounts of data. While statistical analysis provides insight into this data, scientific visualization is tactically important for scientific discovery, product design and data analysis. These benefits are impeded, however, when scientific visualization algorithms are implemented from scratch — a time-consuming and redundant process in immersive application development. This process can greatly benefit from leveraging the state-of-the-art open-source Visualization Toolkit (VTK) and its community. Over the past two (almost three) decades, integrating VTK with a virtual reality (VR) environment has only been attempted to varying degrees of success. In this paper, we demonstrate two new approaches to simplify this amalgamation of an immersive interface with visualization rendering from VTK. In addition, we cover several enhancements to VTK that provide near real-time updates and efficient interaction. Finally, we demonstrate the combination of VTK with both Vrui and OpenVR immersive environments in example applications.